Search found 157 matches

by xiaogenz
Mon Oct 09, 2023 1:23 am
Forum: Main Forum
Topic: Edock standalone
Replies: 2
Views: 16287

Re: Edock standalone

Currently, Edock only supports Python 2. We plan to provide an update for compatibility with Python 3 in the near future.
by xiaogenz
Tue Sep 26, 2023 11:06 pm
Forum: Main Forum
Topic: problem in running demo
Replies: 25
Views: 316668

Re: problem in running demo

DEMO uses CPU for running.
by xiaogenz
Wed Sep 20, 2023 5:45 am
Forum: Main Forum
Topic: problem in running demo
Replies: 25
Views: 316668

Re: problem in running demo

Okay! I think it can be correctly run now. Please let me know if you have any questions.
by xiaogenz
Sun Sep 17, 2023 7:48 am
Forum: Main Forum
Topic: problem in running demo
Replies: 25
Views: 316668

Re: problem in running demo

The first nr is your folder name and the second nr is the file name in the folder. Same as uniclust30_2017_04. The settings of DEMO is correct now. But you should also change the settings of hhblitsdb, jackhmmerdb, and hmmsearchdb (lines 32-35) in /mdia/ravis/data/DEMO/external/runDistPre.pl. Otherw...
by xiaogenz
Sat Sep 16, 2023 2:38 am
Forum: Main Forum
Topic: problem in running demo
Replies: 25
Views: 316668

Re: problem in running demo

Please change your settings to: NR_DB = "/mdeia/ravis/data/DEMO/local_library/nr/nr" hhblitsdb = "/mdeia/ravis/data/DEMO/local_library/uniclust30_2017_04/uniclust30_2017_04" jackhmmerdb = "/mdeia/ravis/data/DEMO/local_library/uniref90.fasta/uniref90.fasta" hmmsearchdb =...
by xiaogenz
Thu Sep 14, 2023 7:03 am
Forum: Main Forum
Topic: problem in running demo
Replies: 25
Views: 316668

Re: problem in running demo

Could you please show me the settings of NR_DB, hhblitsdb, jackhmmerdb, hmmsearchdb, and MDlibpath in lines 55-59 of runDEMO.py.
And please show me the content in local_library folder.

Best wishes,
Xiaogen
by xiaogenz
Thu Sep 14, 2023 2:24 am
Forum: Main Forum
Topic: Sampling rate in EM-refiner
Replies: 3
Views: 14537

Re: Sampling rate in EM-refiner

Hello, '5.0 0.0' is two different parameters, 5.0 is the resolution of density map that you use in the program. the resolution should be change according to the density map. 0.0 is unsampling rate that it don't need to change in the program. By the way, we haven't developed a parallel version. Thank...
by xiaogenz
Wed Sep 13, 2023 5:51 am
Forum: Main Forum
Topic: Sampling rate in EM-refiner
Replies: 3
Views: 14537

Re: Sampling rate in EM-refiner

Hello,

sampling rate is downsampling rate for the density map. it is used to speed up the refinement, but will reduce the accuracy of the refinement. We don't use it in the program. 0.0 means we don't do downsampling in the program.

Thanks,
Biao
by xiaogenz
Mon Sep 11, 2023 1:45 am
Forum: Main Forum
Topic: problem in running demo
Replies: 25
Views: 316668

Re: problem in running demo

Please carefully check lines 56 and 161 in 'run_DEMO2.py'. Ensure that 'hhblitsdb + "_a3m_db"' exists in your library. It's important to note that in line 56, 'hhblitsdb' should be set as your 'uniclust30' directory plus 'uniclust30_2017_04'.

Thanks,
Xiaogen
by xiaogenz
Wed Sep 06, 2023 2:38 am
Forum: Main Forum
Topic: problem in running demo
Replies: 25
Views: 316668

Re: problem in running demo

Please rename your 'uniclust30' folder to 'uniclust30_2017_04'. Otherwise, the program won't be able to locate 'uniclust30_2017_04_a3m_db'. You can refer to line 161 in the 'runDEMO.py' script for clarification.